Fix SNV density and dN/dS in the sample-set SNV search, and revive its test suite - #20

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jbrestel wants to merge 30 commits into

dnaseq-merge-experiments

Commits on Aug 5, 2026

Add the HSSS variation plumbing design spec

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97ba19d
Add the HSSS variation plumbing plan; correct the spec's test claims

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5550c41
Build variation IDs with an underscore separator

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Add plan Task 1b: the second ID-composition site

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Build variation IDs with an underscore in the locations filter too

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Fix a plan grep that could only fail, and record two Task 1b findings

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Read HSSS variation data from the dnaseq directory

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Record hsssCopyFilesToWebSvcDir as a deliberate non-goal

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Name the strain filter param for variations, not snps

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e463567
Defer FindMajorAllelesPlugin's param rename to its own search's spec

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371db4a
Update HSSS fixtures to the variation ID convention

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7f7d970
Correct Task 6's conifer invocation and config path

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Mark the HSSS variation plumbing spec implemented

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Rename the chromosome param contract for variation searches
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Rename the two sample-group param contracts for variation searches
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9ff40ae

Commits on Aug 6, 2026

Merge remote-tracking branch 'origin/master' into dnaseq-merge-experiments
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6b69766

Commits on Aug 8, 2026

Accept noncoding as an SNP class in FindGenesWithSnpCharsPlugin

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6758ae0
Design: fix the two broken statistics in the HSSS gene characteristics search

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fbf69a8
Plan: implement the HSSS gene statistics fix

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test: pass the missing reconstruct/prefix/suffix args in hsssTestSuite

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Plan: add Task 0 and record the test suite breakage left unfixed

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test: cover all four product classes and re-baseline the HSSS fixtures

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Plan: correct the exit-code assertion and record the majorAlleles off-by-one

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test: add normalizer columns to the geneChars fixture
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Compute CDS density and site-normalized dN/dS in the geneChars filter
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Plan: warn that hsssTestSuite tests the installed copy, not the checkout

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25c6306
Feed per-gene normalizers to the geneChars filter and read its ninth column

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7a61e99
Plan: correct Task 5 scope and record the dormant chip-plugin coupling
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Record the whole-cohort validation of the corrected geneChars statistics

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Merge branch 'feature/hsss-noncoding-class' into dnaseq-merge-experiments
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